title: A pseudo-atomic model for the capsid shell of bacteriophage lambda using chemical cross-linking/mass spectrometry and molecular modeling.
abstract: Bacteriophage lambda is one of the most exhaustively studied of the double-stranded DNA viruses. Its assembly pathway is highly conserved among the herpesviruses and many of the bacteriophages, making it an excellent model system. Despite extensive genetic and biophysical characterization of many of the lambda proteins and the assembly pathways in which they are implicated, there is a relative dearth of structural information on many of the most critical proteins involved in lambda assembly and maturation, including that of the lambda major capsid protein. Toward this end, we have utilized a combination of chemical cross-linking/mass spectrometry and computational modeling to construct a pseudo-atomic model of the lambda major capsid protein as a monomer, as well as in the context of the assembled procapsid shell. The approach described here is generalizable and can be used to provide structural models for any biological complex of interest. The procapsid structural model is in good agreement with published biochemical data indicating that procapsid expansion exposes hydrophobic surface area and that this serves to nucleate assembly of capsid decoration protein, gpD. The model further implicates additional molecular interactions that may be critical to the assembly of the capsid shell and for the stabilization of the structure by the gpD decoration protein.
authors.affiliation: Department of Medicinal Chemistry, School of Pharmacy, University of Washington, H-172 Health Sciences Building, Box 357610, Seattle, WA 98195, USA.
authors.forename: Pragya
authors.initials: P
authors.lastname: Singh
authors.forename: Eri
authors.initials: E
authors.lastname: Nakatani
authors.forename: David R
authors.initials: DR
authors.lastname: Goodlett
authors.forename: Carlos Enrique
authors.initials: CE
authors.lastname: Catalano
mesh_terms: D000595:Amino Acid Sequence; D010582:Bacteriophage lambda / Q000737:chemistry / Q000187:drug effects / Q000502:physiology* / Q000648:ultrastructure; D002213:Capsid / Q000737:chemistry* / Q000187:drug effects / Q000378:metabolism / Q000648:ultrastructure; D036022:Capsid Proteins / Q000737:chemistry* / Q000187:drug effects / Q000378:metabolism*; D003432:Cross-Linking Reagents / Q000494:pharmacology; D006023:Glycoproteins / Q000737:chemistry / Q000378:metabolism; D013058:Mass Spectrometry / Q000379:methods; D008954:Models, Biological; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D055503:Protein Multimerization / Q000502:physiology; D055550:Protein Stability / Q000187:drug effects; D020836:Protein Structure, Quaternary; D054928:Validation Studies as Topic; D019065:Virus Assembly / Q000187:drug effects / Q000502:physiology
chemical_list: D036022:Capsid Proteins; D003432:Cross-Linking Reagents; D006023:Glycoproteins; C406073:gpD protein, lambda phage
keywords: 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide HCl; BS2; CID; CXMS; DNA packaging; EDC; MS; NHS-diazirine (succinimidyl 4,4′-azipentanoate); SDA; bacteriophage lambda; bis(sulfosuccinimidyl)glutarate; capsid assembly; chemical cross-linking/mass spectrometry; collision-induced dissociation; cryo-EM; cryo-electron microscopy; double-stranded DNA; dsDNA; mass spectrometry; virus assembly; virus structure